def create_sample(session, metadata):
study, new = funcs.get_or_create(
session, Study, name=metadata['study_name'])
if new:
logger.info('Created new study "{}"'.format(study.name))
session.commit()
sample, new = funcs.get_or_create(
session, Sample, name=metadata['sample_name'], study=study)
if new:
logger.info('Created new sample "{}"'.format(sample.name))
for key, value in metadata.items():
if key not in REQUIRED_FIELDS:
session.add(SampleMetadata(
sample=sample,
key=key,
value=value
))
subject, new = funcs.get_or_create(
session, Subject, study=study,
identifier=metadata['subject'])
sample.subject = subject
session.commit()
else:
logger.error(
'Sample "{}" already exists'.format(metadata['sample_name']))
return
return sample
def run_import(session, args, remaps=None):
v_germlines = VGermlines(args.v_germlines)
j_germlines = JGermlines(args.j_germlines, args.upstream_of_cdr3,
args.anchor_len, args.min_anchor_len)
study, new = funcs.get_or_create(session, Study, name=args.study_name)
if new:
logger.info('Created new study "{}"'.format(study.name))
session.commit()
sample, new = funcs.get_or_create(session,
Sample,
name=args.sample_name,
study=study)
if new:
sample.date = args.date
logger.info('Created new sample "{}"'.format(sample.name))
for key in ('subset', 'tissue', 'disease', 'lab', 'experimenter',
'ig_class', 'v_primer', 'j_primer'):
setattr(sample, key, vars(args).get(key, None))
subject, new = funcs.get_or_create(session,
Subject,
study=study,
identifier=args.subject)
sample.subject = subject
session.commit()
else:
loger.error('Sample "{}" already exists'.format(args.sample_name))
return
with open(args.input_file) as fh:
read_file(session, fh, sample, v_germlines, j_germlines, args, remaps)
def _setup_sample(self, meta):
self._sync_lock.acquire()
self._session.commit()
study, new = funcs.get_or_create(self._session,
Study,
name=meta['study_name'])
if new:
self.info('\tCreated new study "{}"'.format(study.name))
self._session.commit()
name = meta['sample_name']
sample, new = funcs.get_or_create(self._session,
Sample,
name=name,
study=study)
if new:
sample.date = meta['date']
self.info('\tCreated new sample "{}"'.format(sample.name))
for key in ('subset', 'tissue', 'disease', 'lab', 'experimenter',
'ig_class', 'v_primer', 'j_primer'):
setattr(sample, key, meta.get(key, None))
subject, new = funcs.get_or_create(self._session,
Subject,
study=study,
identifier=meta['subject'])
sample.subject = subject
self._session.commit()
self._sync_lock.release()
return study, sample
def setup_sample(session, meta):
study, new = funcs.get_or_create(session, Study, name=meta['study_name'])
if new:
logger.info('Created new study "{}"'.format(study.name))
session.commit()
name = meta['sample_name']
sample, new = funcs.get_or_create(session, Sample, name=name, study=study)
if new:
subject, new = funcs.get_or_create(session,
Subject,
study=study,
identifier=meta['subject'])
sample.subject = subject
for key, value in meta.items():
if key not in REQUIRED_FIELDS:
session.add(SampleMetadata(sample=sample, key=key,
value=value))
session.commit()
return sample
def setup_sample(session, meta):
study, new = funcs.get_or_create(session, Study, name=meta['study_name'])
if new:
logger.info('Created new study "{}"'.format(study.name))
session.commit()
name = meta['sample_name']
sample, new = funcs.get_or_create(session, Sample, name=name, study=study)
if new:
subject, new = funcs.get_or_create(
session, Subject, study=study,
identifier=meta['subject'])
sample.subject = subject
for key, value in meta.items():
if key not in REQUIRED_FIELDS:
session.add(SampleMetadata(
sample=sample, key=key, value=value
))
session.commit()
return sample